GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Herbaspirillum seropedicae SmR1

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate HSERO_RS19990 HSERO_RS19990 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__HerbieS:HSERO_RS19990
          Length = 400

 Score =  577 bits (1486), Expect = e-169
 Identities = 289/401 (72%), Positives = 338/401 (84%), Gaps = 1/401 (0%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M +  I DA+RTPIGRY GAL  VRADDLGA+PL+AL+ R+PQ+DW AVDDVIYGCANQA
Sbjct: 1   MKDVFICDAIRTPIGRYGGALKDVRADDLGAVPLRALMERNPQVDWKAVDDVIYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ LLAGLP  VPG+T+NRLCGSG+DA+G+AARA++ GE  LM+AGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPQEVPGSTINRLCGSGMDALGTAARAIKSGETQLMIAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           +RAPFVMGK++ AF R A I DTTIGWRFVN LM+Q +G+D+MPETAENVA  F +SRAD
Sbjct: 121 TRAPFVMGKADSAFSRQAAIQDTTIGWRFVNALMKQKYGVDAMPETAENVAVDFKVSRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QD FA+RSQ KAAAA ANG LA+EIV V I Q+KG    V  DEHPR  T++E LA+L  
Sbjct: 181 QDQFAVRSQAKAAAAQANGTLAQEIVPVVIPQKKGDPITVTQDEHPRA-TSMEALARLKG 239

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
             +  GSVTAGNASGVNDGACALLLAS+EA +++ LK RAR++GMATAGV PRIMG+GP 
Sbjct: 240 VVKPDGSVTAGNASGVNDGACALLLASAEAVEKYQLKPRARILGMATAGVAPRIMGMGPA 299

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PA++KVL   G+ +  MDVIELNEAFA+QGLAVLRELG+ADDD RVNPNGGAIALGHPLG
Sbjct: 300 PASKKVLAQLGMTIDQMDVIELNEAFASQGLAVLRELGVADDDARVNPNGGAIALGHPLG 359

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTA ++LE   GRYALCTMCIGVGQGIA++IER+
Sbjct: 360 MSGARLVTTATYQLERTGGRYALCTMCIGVGQGIAMVIERV 400


Lambda     K      H
   0.319    0.134    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 549
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate HSERO_RS19990 HSERO_RS19990 (acetyl-CoA acetyltransferase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.14080.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14080.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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